阮玨課題組

Ruan Jue Lab

課題組長

阮玨，研究員，博士生導(dǎo)師，農(nóng)業(yè)基因組學(xué)技術(shù)研發(fā)與應(yīng)用創(chuàng)新團(tuán)隊(duì)首席科學(xué)家，長期專注于基因組組裝問題，主導(dǎo)開發(fā)的三代測序數(shù)據(jù)組裝與序列比對算法SMARTdenovo、wtdbg和bsalign，突破了三代數(shù)據(jù)組裝速度落后于測序速度的領(lǐng)域難題，成為三代測序組裝的主流算法。以第一/通訊作者（含并列）在Nature、Cell、Nature Methods、National Science Review、Nature Communications等國際學(xué)術(shù)期刊上發(fā)表論文30余篇，所有論文累計(jì)被引4萬余次（Scopus）。

工作經(jīng)歷

2017.5 至今                     中國農(nóng)業(yè)科學(xué)院農(nóng)業(yè)基因組研究所                        研究員

2014.5 至 2017.4            中國農(nóng)業(yè)科學(xué)院深圳農(nóng)業(yè)基因組研究所                  研究員

2012.1 至 2014.4            中國科學(xué)院北京基因組研究所                               副研究員

2009.7 至 2011.12          中國科學(xué)院北京基因組研究所                               助理研究員

 

教育經(jīng)歷

中國科學(xué)院北京基因組研究所           生物信息學(xué)        博士             2004.9 - 2009.7

南開大學(xué)                                         生物科學(xué)            學(xué)士             2000.9 - 2004.7

 

課題組成員

研究方向	學(xué)生	科研助理
基因組算法開發(fā)	王曉波、張妍、宗培玉、鄧文鵬、張勇、李新慧、劉帆波	伍世剛、劉海琳、于洋
表型組算法開發(fā)	常建業(yè)、劉秉文、潘禹辰、董林森、候登峰、程豪（客座）
DNA存儲技術(shù)	丁璐璐、許亞蘋
測序方法研發(fā)	侯志浩、張婭、關(guān)欣悅
生物信息分析	周紅玲、吳越（客座）	艾成、李阿倫、宋艷妮

課題組聯(lián)系方式: 阮玨 <[email protected]>、謝欣<<>[email protected]>

研究方向:

課題組主要從事組學(xué)算法研發(fā)：1）開發(fā)快速精準(zhǔn)的序列比對與組裝算法開發(fā)；2）開發(fā)高效的圖基因組構(gòu)建與分析流程；3）制備圖像表型標(biāo)準(zhǔn)數(shù)據(jù)集，搭建共享平臺，開發(fā)植物表型圖像識別算法；4）開發(fā)具有高糾錯(cuò)能力的DNA數(shù)字存儲算法；5）拓展測序方法研發(fā)：如低頻突變檢測，宏基因組測序等；6）在組學(xué)算法研發(fā)的基礎(chǔ)上，進(jìn)一步開展生物信息學(xué)研究，為組學(xué)算法的深入利用提供支撐。

研究進(jìn)展：

課題組針對最新的測序技術(shù)，以序列比對與基因組組裝技術(shù)為重點(diǎn)，展開了多個(gè)重難點(diǎn)算法與軟件的開發(fā)與應(yīng)用，推動了數(shù)項(xiàng)重大合作研究的順利進(jìn)行。

重要進(jìn)展成果1：率先提出了將256個(gè)連續(xù)堿基合并為一個(gè)基本比對單元的長序列比對思路（kmer-bin-mapping），顯著提高了測序數(shù)據(jù)的比對速度，并開發(fā)了三代長序列組裝算法WTDBG，在保證組裝結(jié)果的連續(xù)性和準(zhǔn)確性下，極大地提高了第三代數(shù)據(jù)的組裝速度，首次將數(shù)據(jù)分析時(shí)間降低到少于數(shù)據(jù)產(chǎn)出時(shí)間；

重要進(jìn)展成果2：提出被廣泛使用的同聚堿基壓縮方法SMARTdenovo，實(shí)現(xiàn)了高效率三代長序列組裝，該算法能夠在3,000 核心小時(shí)（CPU * hours）內(nèi)完成人類基因組組裝，效率較早期算法HGAP提高100多倍。2015年起SMARTdenovo供領(lǐng)域開源使用，是早期納米孔測序組裝的首選組裝算法；

重要進(jìn)展成果3：先后與多個(gè)科研院所及高校進(jìn)行了以基因組學(xué)技術(shù)為支撐的項(xiàng)目合作，在Nature、Cell、Cell Research、Nature Genetics、Nature Methods、Nature Communications、National Science Review、Genome Research等期刊上發(fā)表一系列文章，在領(lǐng)域內(nèi)均有較高的引用率。

 

代表論文:

(1) Chentao Yang#, Yang Zhou#, Yanni Song#, Dongya Wu#, Yan Zeng#, Lei Nie, Panhong, Liu,Shilong Zhang, Guangji Chen, Jinjin Xu, Hongling Zhou, Long Zhou, Xiaobo Qian, Chenlu Liu, Shangjin Tan,Chengran Zhou, Wei Dai, Mengyang Xu, Yanwei Qi, Xiaobo Wang, Lidong Guo, Guangyi Fan, Aijun Wang, Yuan Deng, Yong Zhang, Jiazheng Jin, Yunqiu He, Chunxue Guo, Guoji Guo, Qing Zhou, Xun Xu, Huanming Yang, Jian Wang, Shuhua Xu, Yafei Mao,Xin Jin, Jue Ruan*and Guojie Zhang*. "The complete and fully-phased diploid genome of a male Han Chinese."Cell Research. 2023,0:1–17.

(2) Yong Zhang#, Hong-Wei Lu#, Jue Ruan*. "GAEP: a comprehensive genome assembly evaluating pipeline."Journal of Genetics and Genomics.2023,0:1-8.

(3) Lianguang Shang#, Xiaoxia Li#, Huiying He#, Qiaoling Yuan#, Yanni Song#, Zhaoran Wei#, Hai Lin#, Min Hu#, Fengli Zhao#,Chao Zhang, Yuhua Li, Hongsheng Gao, Tianyi Wang, Xiangpei Liu, Hong Zhang, Ya Zhang, Shuaimin Cao, Xiaoman Yu, Bintao Zhang, Yong Zhang, Yiqing Tan, Mao Qin, Cheng Ai, Yingxue Yang, Bin Zhang, Zhiqiang Hu, Hongru Wang, Yang Lv, Yuexing Wang, Jie Ma, Quan Wang, Hongwei Lu, Zhe Wu, Shanlin Liu, Zongyi Sun, Hongliang Zhang, Longbiao Guo, Zichao Li, Yongfeng Zhou ,Jiayang Li,Zuofeng Zhu*, Guosheng Xiong*, Jue Ruan*,Qian Qian*."A super pan-genomic landscape of rice."Cell Research. 2022,32(10): 878-896.

(4) Dingyu Yan*, Xier Luo#, Jiabin Tang#, Shanghua Xu, Kongwei Huang, Xiaobo Wang, Tong Feng, Tengcheng Que, Miaomiao Jia, Xiaobing Guo, Saif ur Rehman, Zhipeng Li, Yufeng Yang, Kaixiang Li, Kuiqing Cui, Jue Ruan*, and Qingyou Liu*. "High-Quality Genomes of Pangolins: Insights into the Molecular Basis of Scale Formation and Adaption to Myrmecophagous Diet."Molecular Biology and Evolution, 2022,40(1):1-15.

(5) Yong Shao*, Xiao-Bo Wang#, Mei-Ling Zhang#, Yan Liu#, Sheng Wang, Bao-Lin Zhang, Min-Min Yang, Ming-Hai Yang, Ting Jia, Tian-Chun Pu, Yan Lu, He Liu, Zhe Xu, Bo Li, Ning Liu, Violet Magoma Onsongo, Dong-Dong Wu, Cheng-Lin Zhang*, Jue Ruan*, and Yan Li*. "Long-Read Genome Sequencing Provides Molecular Insights into Scavenging and Societal Complexity in Spotted Hyena Crocuta crocuta. "Molecular Biology and Evolution, 2022,39(3):1-13.

(6) Xiumei Xing*, Cheng Ai#, Tianjiao Wang#, Yang Li#, Huitao Liu#, Pengfei Hu#, Guiwu Wang#, Huamiao Liu, Hongliang Wang, Ranran Zhang, Junjun Zheng, Xiaobo Wang, Lei Wang, Yuxiao Chang, Qian Qian, Jinghua Yu, Lixin Tang, Shigang Wu, Xiujuan Shao, Alun Li, Peng Cui, Wei Zhan, Sheng Zhao, Zhichao Wu, Xiqun Shao, Yimeng Dong, Min Rong, Yihong Tan, Xuezhe Cui, Shuzhuo Chang, Xingchao Song, Tongao Yang, Limin Sun, Yan Ju, Pei Zhao, Huanhuan Fan, Ying Liu, Xinhui Wang, Wanyun Yang, Min Yang, Tao Wei, Shanshan Song, Jiaping Xu, Zhigang Yue, Qiqi Liang*, Chunyi Li*, Jue Ruan*, and Fuhe Yang*. "The first high-quality reference genome of sika deer provides insights for high-tannin adaptation."Genomics, Proteomics & Bioinformatics, 2022,21(1):203-215.

(7) Weihua Pan#*, and Jue Ruan#*. "En Route to Completion: What Is An Ideal Reference Genome?"Genomics Proteomics & Bioinformatics, 2022,20(1), 1-3.

(8) Rui Ruan#, Tong Feng#, Ying Li, Huamei Yue, Huan Ye, Hao Du, Qingyou Liu, Jue Ruan*, Chuangju Li*, and Qiwei Wei*. "Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing."Genomics, 2021,113(6).

(9) Xier Luo#, Kuiqing Cui#, Zhiqiang Wang#, Zhipeng Li, Zhengjiao Wu, Weiyi Huang, Xing-Quan Zhu, Jue Ruan*, Weiyu Zhang*, and Qingyou Liu*. "High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions."PLoS Neglected Tropical Diseases, 2021,15(10):1-24.

(10) Hailin Liu#, Xin Han#, Jue Ruan#, Lian Xu#, and Bing He#*. "Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network."Forests, 2021,12(3):1-16.

(11) Hailin Liu#, Xiaobo Wang#, Guibin Wang#, Peng Cui#, Shigang Wu, Cheng Ai, Nan Hu, Alun Li, Bing He, Xiujuan Shao, Zhichao Wu, Hu Feng, Yuxiao Chang, Desheng Mu, Jing Hou, Xiaogang Dai, Tongming Yin*, Jue Ruan*, and Fuliang Cao*. "The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution."Nature Plants, 2021, 7 (6): 748-+..

(12) Hailin Liu#, Shigang Wu#, Alun Li#, and Jue Ruan*. "SMARTdenovo: a de novo assembler using long noisy reads."Gigabyte, 2021,2021:15.

(13) Kun Wang#, Jun Wang#, Chenglong Zhu#, Liandong Yang#, Yandong Ren#, Jue Ruan#, Guangyi Fan#, Jiang Hu#, Wenjie Xu, Xupeng Bi, Youan Zhu, Yue Song, Huatao Chen, Tiantian Ma, Ruoping Zhao, Haifeng Jiang, Bin Zhang, Chenguang Feng, Yuan Yuan, Xiaoni Gan, Yongxin Li, Honghui Zeng, Qun Liu, Yaolei Zhang, Feng Shao, Shijie Hao, He Zhang, Xun Xu, Xin Liu, Depeng Wang, Min Zhu, Guojie Zhang, Wenming Zhao*, Qiang Qiu*, Shunping He*, and Wen Wang*. "African lungfish genome sheds light on the vertebrate water-to-land transition."Cell, 2021,184(5), 1362-1376.

(14) Fengli Zhao#, Yuexing Wang#, Jianshu Zheng#, Yanling Wen, Minghao Qu, Shujing Kang, Shigang Wu, Xiaojuan Deng, Kai Hong, Sanfeng Li, Xing Qin, Zhichao Wu, Xiaobo Wang, Cheng Ai, Alun Li, Longjun Zeng ,Jiang Hu, Dali Zeng, Lianguang Shang, Quan Wang, Qian Qian, Jue Ruan* and Guosheng Xiong*. "A Genome-Wide Survey of Copy Number Variations Reveals an Asymmetric Evolution of Duplicated Genes in Rice."BMC Biology， 2020.26;18(1):73.

(15) Xinchao Wang#, Hu Feng#, Yuxiao Chang#, Chunlei Ma#, Liyuan Wang#, Xinyuan Hao#, A lun Li, Hao Cheng, Lu Wang, Peng Cui, Jiqiang Jin, Xiaobo Wang, Kang Wei, Cheng Ai, Sheng Zhao, Zhichao Wu, Youyong Li, Benying Liu, Guo-Dong Wang*, Liang Chen*, Jue Ruan* and Yajun Yang*. "Population sequencing enhances understanding of tea plant evolution."Nature Communications，2020,7;11(1):4447.

(16) Jing Luo #, Jing Chai#, Yanling Wen#, Min Tao#, Guoliang Lin#, Xiaochuan Liu, Li Ren, Zeyu Chen, Shigang Wu, Shengnan Li, Yude Wang, Qinbo Qin, Shi Wang, Yun Gao, Feng Huang, Lu Wang, Cheng Ai, Xiaobo Wang, Lianwei Li, Chengxi Ye, Huimin Yang, Mi Luo, Jie Chen, Hong Hu, Liujiao Yuan, Li Zhong, Jing Wang, Jian Xu, Zhenglin Du, Zhanshan Sam Ma,  Robert W.Murphy, Axel Meyer, Jianfang Gui, Peng Xu*, Jue Ruan*, Z.Jeffrey Chen*, Shaojun Liu*, Xuemei Lu*, Ya-ping Zhang*. "From asymmetrical to balanced genomic diversification during rediploidization: subgenomic evolution in allotetraploid fish."Science Advance. 2020.6,22:7677.

(17) Yong Shao#, Xiaobo Wang#, Jinjin Zhang#, Mingli Li#, Shousong Wu, Xiyao Ma, Xue Wang, Huifang Zhao, Yuan Li, Helenhe Zhu, David M. Irwin, Depeng Wang, Guojie Zhang*, Jue Ruan*, Dongdong Wu*."Genome and single-cell RNA-sequencing of the earthworm Eisenia andrei identifies cellular mechanisms underlying regeneration."Nature Communications. 2020,11(1):2656.

(18) Xier Luo#, Yu Zhou#, Bing Zhang#, Yi Zhang#, Xiaobo Wang, Tong Feng , Zhipeng Li, Kuiqing Cui, Zhiqiang Wang, Chan Luo, Hui Li, Yanfei Deng, Fenghua Lu, Jianlin Han, Yongwang Miao, Huaming Mao, Xiaoyan Yi, Cheng Ai, Shigang Wu, Alun Li, Zhichao Wu, Zijun Zhuo, Do DaGiang, Bikash Mitra, Mohammad Farhad Vahidi, Shahid Mansoor, Sahar Ahmed Al-Bayatti, Eka Meutia Sari, Neena Amatya Gorkhali, Sigit Prastowo, Laiba Shafique, Guoyou Ye, Qian Qian, Baoshan Chen, Deshun Shi*, Jue Ruan* and Qingyou Liu*. “Understanding divergent domestication traits from the whole-genome sequencing of swamp and river buffalo populations."National Science Review, 2020.7,3:686-701.

(19) Jue Ruan?* and Heng Li*."Fast and accurate long-read assembly with wtdbg2."Nature Methods, 2020.17:155–158.

(20) Mao Qin#, Shigang Wu, Alun Li, Fengli Zhao, Hu Feng, Lulu Ding and Jue Ruan*."LRScaf: improving draft genomes using long noisy reads."BMC Genomics, 2019.201:955.

(21) Wensheng Wang#, Ramil Mauleon#, Zhiqiang Hu#, Dmytro Chebotarov#, Shuaishuai Tai#, Zhichao Wu#, Min Li#, Tianqing Zheng#, Roven Rommel Fuentes#, Fan Zhang#, locedie Mansueto#, Dario Copetti#, Millicent Sanciangco, Kevin Christian Palis, Jianlong Xu, Chen Sun, Binying Fu, Hongliang Zhang, Yongming Gao, Xiuqin Zhao, Fei Shen, Xiao Cui, Hong Yu, Zichao Li, Miaolin Chen, Jeffrey Detras, Yongli Zhou, Xinyuan Zhang, Yue Zhao, Dave Kudrna, Chunchao Wang, Rui Li, Ben Jia, Jinyuan Lu, Xianchang He, Zhaotong Dong, Jiabao Xu, Yanhong Li, Miao Wang, Jianxin Shi, Jing Li, Dabing Zhang, Seunghee Lee, Wushu Hu, Alexander Poliakov, Inna Dubchak, Victor Jun Ulat, Frances Nikki Borja, John Robert Mendoza, Jauhar Ali, Jing Li, Qiang Gao, Yongchao Niu, Zhen Yue, Ma. Elizabeth B. Naredo, Jayson Talag, Xueqiang Wang, Jinjie Li, Xiaodong Fang, Ye Yin, Jean-Christophe Glaszmann, Jianwei Zhang, Jiayang Li, Ruaraidh Sackville Hamilton, Rod A. Wing*, Jue Ruan*, Gengyun Zhang*, Chaochun Wei*, Nickolai Alexandrov*, Kenneth. McNally*, Zhikang Li*, Hei Leung. "Genomic variation in 3,010 diverse accessions of Asian cultivated rice."Nature, 2018.557(7703): 43-49.

(22) Guodong Wang#, Xiujuan Shao#, Bing Bai#, Junlong Wang, Xiaobo Wang, Xue Cao, Yanhu Liu, Xuan Wang, Tingting Yin, Shaojie Zhang, Yan Lu, Zechong Wang, Lu Wang, Wenming Zhao, Bing Zhang, Jue Ruan*, Yaping Zhang*. "Structural variation during dog domestication: insights from grey wolf and dhole genomes."National Science Review, 2018.6,（1）:110–122.

(23) Tao Lin#, Xia Xu#, Jue Ruan#, Shizhong Liu, Shigang Wu, Xiujuan Shao, Xiaobo Wang, Lin Gan, Bi Qin, Yushuang Yang, Zhukuan Cheng, Suhua Yang, Zhonghua Zhang, Guosheng Xiong, Sanwen Huang, Hong Yu* and Jiayang Li *. “Genome Analysis of Taraxacum Kok-Saghyz Rodin Provides New Insights into Rubber Biosynthesis.”National Science Review, 2018.5(1):78–87.

(24) KaiLe Wang#, Shujuan Lai, Xiaoxu Yang, Tianqi Zhu, Xuemei Lu, Chung-I. Wu*, Jue Ruan*."Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq."Nature Communications, 2017,8:

(25) Zechen Chong#, Jue Ruan#, Min Gao#, Wanding Zhou, Tenghui Chen, Xian Fan, Li Ding, Anna Y Lee, Paul Boutros, JunJie Chen, Ken Chen*. "novoBreak: local assembly for breakpoint detection in cancer genomes."Nature Methods, 2017. 14(1): 65-67.

(26) Li Yu#, Guodong Wang#, Jue Ruan#, Yongbin Chen#, Cuiping Yang#, Xue Cao#, Hong Wu#, Yanhu Liu#, Zhenglin Du#, Xiaoping Wang#, Jing Yang#, Shaochen Cheng#, Li Zhong, Lu Wang, Xuan Wang, Jingyang Hu, Lu Fang, Bing Bai, Kaile Wang, Na Yuan, Shifang Wu, Baoguo Li, Jinguo Zhang, Yeqin Yang, Chenglin Zhang, Yongcheng Long, Haishu Li, Jingyuan Yang, David M Irwin, Oliver A Ryder, Ying Li*, Chung-I Wu*, Yaping Zhang*. "Genomic analysis of snub-nosed monkeys Rhinopithecus identifies genes and processes related to high-altitude adaptation."Nature Genetics, 2016.48(8):947-952.

(27) Kaile Wang#, Qin Ma, Lan Jiang, Shujuan Lai, Xuemei Lu, Yali Hou, Chung-I. Wu*, Jue Ruan*. "Ultra-precise detection of mutations by droplet-based amplification of circularized DNA."BMC Genomics, 2016.17

(28) Kaile Wang#, Xiaolu Ma#, Xue Zhang, Dafei Wu, Chenyi Sun, Yazhou Sun, Xuemei Lu, Chung-I. Wu*, Caixia Guo*, Jue Ruan*. "Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis."Scientific Reports, 2016.6: 25310.

代表專利：

(1) 李瑞強(qiáng);阮玨;朱紅梅;李松崗;王俊;楊煥明;汪健.一種組裝基因組的方法,2011-6-29，中國，CN200810218338.9（授權(quán)）,獲國家優(yōu)秀專利獎

(2) 阮玨;王開樂;呂雪梅;吳仲義.測序文庫及其制備和應(yīng)用,2017-10-20,中國，CN201310651462.5（授權(quán)）（國際專利同號）

(3) 阮玨;王開樂;沈栩;呂雪梅;吳仲義.一種DNA擴(kuò)增方法,2019-5-17，中國，

CN201410448896.X（授權(quán)）

(4) 王開樂;阮玨;呂雪梅;吳仲義.改進(jìn)的測序文庫及其制備和應(yīng)用，2019-10-15，中國，CN201410448968.0（授權(quán)）

(5) 阮玨;王開樂.測序文庫及其制備和應(yīng)用，2020-4-21，中國，CN201510638417.5（授權(quán)）

(6) 阮玨;王開樂;吳仲義;呂雪梅.測序文庫及其制備和應(yīng)用，2020-7-21，US10718015B2（國際專利）

(7) 劉慶友;羅西爾;阮玨;石德順;周宇;崔奎青;李志鵬;李輝;馮彤;王曉波.一種基于全基因組SNP信息追溯水牛血統(tǒng)來源以及進(jìn)行基因組選配的方法，2022-12-06，中國，CN202010198365.5（授權(quán)）

(8) 阮玨;王開樂.測序文庫及其制備和應(yīng)用，2023-7-18，US11702690（國際專利）

(9) 阮玨;侯志浩;王開樂;常玉曉;李阿倫.核酸檢測試劑盒、反應(yīng)體系及方法，2021-09-15，中國，CN202111081033.X（申請）

(10) 阮玨;丁璐璐;伍世剛.DNA存儲的軟判決信息譯碼方法及編碼方法，2022-09-14，CN202211116662.6（申請）

(11) 阮玨;陳鵬;常玉曉;郭建飛.一種簡化基因組測序的方法與相關(guān)應(yīng)用，2022-11-01，CN202211356595.5（申請）

(12) 阮玨;來昊政;常建業(yè);王盼盼.基于單目深度估計(jì)的農(nóng)作物株高測量方法，2023-02-09，CN202310152950.5（申請）

獎勵：

1. 2023年獲第八屆中國農(nóng)業(yè)科學(xué)院“十佳青年”；

2. 2022獲“中國農(nóng)業(yè)農(nóng)村重大科技新成果”；

3. 2022獲“中國農(nóng)業(yè)科學(xué)重大進(jìn)展”；

4. 2021年獲“十大重大科學(xué)發(fā)現(xiàn)”；

5. 2021年獲“中國生命科學(xué)十大進(jìn)展”；

6. 2021年獲中國百篇最具影響國際學(xué)術(shù)論文；

7. 2020獲中國生物信息學(xué)十大進(jìn)展；

8. 2020年獲中國農(nóng)業(yè)科學(xué)院“8項(xiàng)重大科學(xué)發(fā)現(xiàn)”；

9. 2020年獲中國農(nóng)業(yè)科學(xué)院“2020年十大科技進(jìn)展”；

10. 2019年獲中國農(nóng)業(yè)科學(xué)院“2019年十大科技進(jìn)展”；

11. 2018年獲“杰出青年農(nóng)業(yè)科學(xué)家”；

12. 2016年獲“中國專利優(yōu)秀獎”。

 

阮玨課題組更新于2023年8月